Annotation Conf. Call 2019-02-12
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- Please see the GO's Google calendar.
- Contact Kimberly if you do not have access.
GOC Meeting, Cambridge, UK
- Thursday, April 11th and Friday, April 12th
- 1/2 day shorter than our usual meetings
- Agenda - start Google doc?
New GOC Website
- Congrats to all who worked on getting the new GOC website out to production
- Any additional comments, feedback, questions?
- Annotation reports on snapshot, current
- Any comments, feedback, questions?
- Ontology editors are collaborating with the Rhea database to align GO and Rhea (and Reactome).
- For enzymatic activities, please check for an existing Rhea reaction xref and add to your request.
References for GO Annotations
- Are papers published on bioRxiv acceptable to use as references for GO annotation?
- Discussion on Twitter:
GOC Progress Report
- Reminder about PMC submission for all articles associated with the GOC grant progress report
GOC Hackathon - Berkeley, January 28th - February 1st
- Working meeting held in Berkeley to develop SOP for importing a MOD's worth of GO annotation into Noctua as gene-centric GO-CAMs
- Details on the outcome of this meeting will be presented on next week's GO-CAM call
- On call: Barbara, Chris, David, Dmitry, Dustin, Edith, Giulia, Helen, Harold, Karen, Kevin M, Kimberly, Li, Michele, Midori, Monika, Patrick N, Rob, Sabrina, Shur-Jen, Seth, Stacia, Suzi A, Tanya, Laurent-Philippe, Petra
GOC Meeting, Cambridge, UK
- Hotel bloc available thru March 1st, so please reserve now if you need a room
- Meeting is Thursday and Friday, but Saturday could be reserved for working groups, if needed - please think about this!
- Registration fees will likely be <100 pounds and Val will look into coordinating payment through her department (otherwise - cash payment at the meeting)
- Please check funding and contributors list for each group
- Report any other issues on the github helpdesk repo
Ontology Requests - Enzymatic Activities
- When requesting a new enzymatic activity term, please check the Rhea database for an appropriate xref and include that with your request
- Please also always include a PMID or other accession/identifier for a reference
- You can search Rhea using an EC
- Rhea is very comprehensive and detailed, but if you believe that the enzymatic activity you're looking for is not included, you can request a new entry from Rhea
Curating Preprints in bioRxiv
- Good discussion on the pros/cons of curating preprints, especially those found in bioRxiv
- Although most groups would not choose to do this right now, we concluded that if a curator feels strongly that there is valuable information in a bioRxiv preprint, they may curate that paper
- Proposed SOP (to be presented on manager's call for final approval):
- Curator should determine that the preprint is the only published source of the data and that the data is of high quality
- GO annotations can be made as usual, citing the unique accession of the preprint
- If and when the preprint appears as a peer-reviewed publication, the curator needs to review the paper again, perhaps in collaboration with the authors, to make certain that the annotations are still correct
- Existing and/or new annotations from the paper will then be updated to cite the accession for the peer-reviewed paper
Other Reference Related Topics
- We discussed how groups handle retracted papers - all annotations associated with retracted papers need to be removed
- Papers where the conclusions may have been over-interpreted or where more recent data has clarified the role or activity of genes - these annotations should be reviewed and removed if no longer accurate
- We still need an effective mechanism for keeping track of papers that should not be (re-)annotated once the data in the paper has been shown to be incorrect
- Could we get a handle on how many papers curated for GO have subsequently been shown to have incorrect information?
- Could we compare older annotation files with new files to see which references have been removed?